RDocumentation
Moon
Learn R
Search all packages and functions
⚠️
There's a newer version (1.18.5) of this package.
Take me there.
VariantAnnotation (version 1.12.9)
Annotation of Genetic Variants
Description
Annotate variants, compute amino acid coding changes, predict coding outcomes
Copy Link
Copy
Link to current version
Version
Version
1.18.5
1.18.1
1.16.1
1.14.13
1.12.9
Down Chevron
Version
1.12.9
License
Artistic-2.0
Maintainer
Valerie Obenchain
Last Published
January 1st, 1970
Functions in VariantAnnotation (1.12.9)
Search functions
VariantAnnotation-defunct
Defunct Functions in Package
VariantAnnotation
genotypeToSnpMatrix
Convert genotype calls from a VCF file to a SnpMatrix object
getTranscriptSeqs
Get transcript sequences
isSNV
Identification of genomic variant types.
GLtoGP
Convert genotype likelihoods to genotype probabilities
PolyPhenDbColumns
PolyPhenDb Columns
predictCoding
Predict amino acid coding changes for variants
locateVariants
Locate variants
PolyPhenDb-class
PolyPhenDb objects
filterVcf
Filter VCF files
probabilityToSnpMatrix
Convert posterior genotype probability to a SnpMatrix object
PROVEANDb-class
PROVEANDb objects
snpSummary
Counts and distribution statistics for SNPs in a VCF object
summarizeVariants
Summarize variants by sample
ScanVcfParam-class
Parameters for scanning VCF files
SIFTDb-class
SIFTDb objects
scanVcf
Import VCF files
SIFTDbColumns
SIFTDb Columns
readVcf
Read VCF files
refLocsToLocalLocs
refLocsToLocalLocs
VRangesList-class
VRangesList objects
writeVcf
Write VCF files
VariantType-class
VariantType subclasses
VCF-class
VCF class objects
VCFHeader-class
VCFHeader instances
VRanges-class
VRanges objects